A fierce argument has been raging over at Barry Arrington’s post, A dog is a chien is a perro is a hund, over whether the genetic code is really a semiotic code, or whether “code” is merely a scientific term of convenience in this case. In this post, I hope to clarify the issues and sharpen the discussion between the two sides.
Let’s begin with Barry Arrington’s argument:
An arrangement of signs is arbitrary when the identical purpose could be accomplished through a different arrangement of signs if the rules of the semiotic code were different…
Here’s an example of an arbitrary arrangement of signs: DOG. This is the arrangement of signs English speakers use when they intend to represent Canis lupus familiaris. … Now, the point is that there is nothing inherent in a dog that requires it to be represented in the English language with the letters “D” followed by “O” followed by “G.” If the rules of the semiotic code (i.e., the English language) were different, the identical purpose could be accomplished through a different arrangement of signs. We know this because in other codes the same purpose is accomplished with vastly different signs. In French the purpose is accomplished with the following arrangement of signs: C H I E N. In Spanish the purpose is accomplished with the following arrangement of signs: P E R R O. In German the purpose is accomplished with the following arrangement of signs: H U N D…
How does this apply to the DNA code? The arrangement of signs constituting a particular instruction in the DNA code is arbitrary in the same way that the arrangement of signs for representing Canis lupus familiaris is arbitrary. For example, suppose in a particular strand of DNA the arrangement “AGC” means “add amino acid X.” There is nothing about amino acid X that requires the instruction “add amino acid X” to be represented by “AGC.” …
Why is all of this important to ID? It is important because it shows that the DNA code is not analogous to a semiotic code. It is isometric with a semiotic code. In other words, the digital code embedded in DNA is not “like” a semiotic code, it “is” a semiotic code. This in turn is important because there is only one known source for a semiotic code: intelligent agency.
In what follows, I’d like to sort out some of the issues relating to whether we can properly speak of a genetic code, and whether talk of a “genetic code” is indispensable to biology. I’ll also look at some objections to the term “genetic code,” before drawing a conclusion as to how the issue might be successfully adjudicated on a scientific basis.
What is “the genetic code”?
Here is how Wikipedia defines the genetic code:
The genetic code is the set of rules by which information encoded within genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences) by living cells. Biological decoding is accomplished by the ribosome, which links amino acids in an order specified by mRNA, using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms, and can be expressed in a simple table with 64 entries.
The code defines how sequences of these nucleotide triplets, called codons, specify which amino acid will be added next during protein synthesis. With some exceptions, a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact some variant codes have evolved. For example, protein synthesis in human mitochondria relies on a genetic code that differs from the standard genetic code.
Is the genetic code just a metaphor, or is it real?
On May 2, 2011, Professor Gregory Chaitin, a world-famous mathematician and computer scientist, gave a talk entitled, Life as Evolving Software. The talk was given at PPGC UFRGS (Portal do Programa de Pos-Graduacao em Computacao da Universidade Federal do Rio Grande do Sul Mestrado), in Brazil. Professor Chaitin is an avowed neo-Darwinist who is currently endeavoring to create a new mathematical version of Darwin’s theory which rigorously proves that evolution can really work. In 2012, Professor Chaitin published a book entitled, Proving Darwin: Making Biology Mathematical (Pantheon, ISBN: 978-0-375-42314-7). Here are some short excerpts from what Professor Chaitin said about the software of life in his talk in May 2011:
[P]eople often talk about DNA as a kind of programming language, and they mean it sort of loosely, as some kind of metaphor, and we all know about that metaphor. It’s especially used a lot, I think, in evo-devo. But it’s a very natural metaphor, because there are lots of analogies. For example, people talk about computer viruses. And another analogy is: there is this sort of principle in biology as well as in the software world that you don’t start over. If you have a very large software project, and it’s years old, then the software tends to get complicated. You start having the whole history of the software project in the software, because you can’t start over… You … can try adding new stuff on top…
So the point is that now there is a well-known analogy between the software in the natural world and the software that we create in technology. But what I’m saying is, it’s not just an analogy. You can actually take advantage of that, to develop a mathematical theory of biology, at some fundamental level…
Here’s basically the idea. We all know about computer programming languages, and they’re relatively recent, right? Fifty or sixty years, maybe, I don’t know. So … this is artificial digital software – artificial because it’s man-made: we came up with it. Now there is natural digital software, meanwhile, … by which I mean DNA, and this is much, much older – three or four billion years. And the interesting thing about this software is that it’s been there all along, in every cell, in every living being on this planet, except that we didn’t realize that … there was software there until we invented software on our own, and after that, we could see that we were surrounded by software…
So this is the main idea, I think: I’m sort of postulating that DNA is a universal programming language. I see no reason to suppose that it’s less powerful than that. So it’s sort of a shocking thing that we have this very very old software around…
So here’s the way I’m looking at biology now, in this viewpoint. Life is evolving software. Bodies are unimportant, right? The hardware is unimportant. The software is important…
In the opinion of this eminent Darwinist scientist, then, talk of a genetic code is quite literal: “it’s not just an analogy.”
Is the information in life quantifiable?
Some ID critics object that the functional complex specified information we see in living things is unquantifiable. However, this criticism can be easily rebutted. The term “functional information” has been rigorously defined by Szostak and his colleagues in recent scientific papers:
1. Hazen, R.M.; Griffin, P.L.; Carothers, J.M.; Szostak, J.W. 2007, Functional information and the emergence of biocomplexity, Proc Natl Acad Sci U S A, 104 Suppl 1, 8574-81.
2. Szostak, J.W. 2003, Functional information: Molecular messages, Nature, 423, (6941) 689.
3. Carothers, J.M.; Oestreich, S.C.; Davis, J.H.; Szostak, J.W. 2004, Informational complexity and functional activity of RNA structures, J Am Chem Soc, 126, (16) 5130-7.
For instance, here is how Hazen, Carothers and Szostak define functional information in the abstract of their 2007 paper:
Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,” I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA–GTP binding energy), I(Ex) = -log2[F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function [greater than or equal to] Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree.
The information in a protein is therefore quantifiable, and has been quantified, as those who are familiar with Dr. Douglas Axe’s work will be aware.
Do we have to speak of a “genetic code”?
On Barry Arrington’s post, A dog is a chien is a perro is a hund, ID critic Alan Fox has proposed that talk of a “genetic code,” while convenient for scientific purposes, is ultimately reducible to chemistry:
Interactions between molecules involve their chemical properties; charge, conformation, level of hydrophilic and lipophilic residues etc. Nothing analogous to language goes on here. (Comment 118)
DNA sequences translate to specific protein sequences by chemical interactions. (Comment 174)
I see no communicative element in the chemical processes that occur when DNA sequences are transcribed into RNA and translated into polypeptide sequences. It’s all a result of the inherent physical and chemical properties of the interacting molecules… To lump chemical processes in with aspects of linguistics is such a stretch that any set that encompasses both is large enough and fuzzy enough to be meaningless… At the cellular and sub-cellular level and consequently and cumulatively at the level of the organism there is a huge amount of communication going on. It is chemical communication… “Encode” could be used as a defined shorthand for some step in the chemical processes that go on in the cell, of course. Maybe there is a scientific definition in the context of biochemistry. (Comment 184)
DNA transcription and translation is a chemical chain of reactions that depends on the spacial conformation and inherent chemical properties of atoms and molecules. (Comment 274)
Eric Anderson challenged Alan Fox at one point in the exchange of opinions:
I hope you aren’t saying that specific protein sequences arise automatically by chemical reactions once the sequence of nucleotides is exposed? There is a whole system in place that takes the 4-character digital code and translates it on the basis of the genetic code into a subsequent physical chain of amino acids. This does not just happen by chemistry. The translation (and it is not just called that by analogy, it is really what is going on) is precisely one of the things that highlights the semiotic nature of the system we are dealing with. (Comment 179)
In a similar vein, Joe responded:
Except there isn’t any physical and chemical properties that DETERMINE which codon REPRESENTS what amino acid. (Comment 192)
Without being uncharitable to Alan Fox, I’d like to get to what seems to me to be the fundamental issue dividing those who insist that talk of a “genetic code” is indispensable to biology from those who say it is not. The critical question, it seems to me, is whether life can be described and explained from the bottom up. What Fox is saying is that we can give from reductionist, bottom-up account which has the same explanatory power as talk of a genetic code. The latter might be more convenient than the former, but is is no more powerful.
If it turns out, then, that the genetic code is a top-down feature of life, then it will indeed be indispensable to biology. But is it? To answer this question, we need to examine the various hypotheses regarding the origin of the genetic code.
Hypotheses regarding the origin of the code
I’d like to quote again from the Wikipedia article on the genetic code, as no-one will accuse Wikipedia of being based in favor of Intelligent Design:
If amino acids were randomly assigned to triplet codons, then there would be 1.5 x 10^84 possible genetic codes to choose from. However, the genetic code used by all known forms of life is nearly universal with few minor variations. This suggests that a single evolutionary history underlies the origin of the genetic code. Many hypotheses on the evolutionary origins of the universal genetic code have been proposed.
Four themes run through the many hypotheses about the evolution of the genetic code:
* Chemical principles govern specific RNA interaction with amino acids. Experiments with aptamers showed that some amino acids have a selective chemical affinity for the base triplets that code for them. Recent experiments show that of the 8 amino acids tested, 6 show some RNA triplet-amino acid association.
* Biosynthetic expansion. The standard modern genetic code grew from a simpler earlier code through a process of “biosynthetic expansion”. Here the idea is that primordial life “discovered” new amino acids (for example, as by-products of metabolism) and later incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer different amino acids were used in the past than today, precise and detailed hypotheses about which amino acids entered the code in what order have proved far more controversial.
* Natural selection has led to codon assignments of the genetic code that minimize the effects of mutations. A recent hypothesis suggests that the triplet code was derived from codes that used longer than triplet codons (such as quadruplet codons). Longer than triplet decoding would have higher degree of codon redundancy and would be more error resistant than the triplet decoding. This feature could allow accurate decoding in the absence of highly complex translational machinery such as the ribosome and before cells began making ribosomes.
* Information channels: Information-theoretic approaches model the process of translating the genetic code into corresponding amino acids as an error-prone information channel. The inherent noise (that is, the error) in the channel poses the organism with a fundamental question: how can a genetic code be constructed to withstand the impact of noise while accurately and efficiently translating information? These “rate-distortion” models suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The code emerges at a coding transition when the mapping of codons to amino-acids becomes nonrandom. The emergence of the code is governed by the topology defined by the probable errors and is related to the map coloring problem.
Transfer RNA molecules appear to have evolved before modern aminoacyl-tRNA synthetases, so the latter cannot be part of the explanation of its patterns.
There are enough data to refute the possibility that the genetic code was randomly constructed (“a frozen accident”). For example, the genetic code clusters certain amino acid assignments. Amino acids that share the same biosynthetic pathway tend to have the same first base in their codons. Amino acids with similar physical properties tend to have similar codons. A robust hypothesis for the origin of genetic code should also address or predict the following gross features of the codon table:
1. absence of codons for D-amino acids
2. secondary codon patterns for some amino acids
3. confinement of synonymous positions to third position
4. limitation to 20 amino acids instead of a number closer to 64
5. relation of stop codon patterns to amino acid coding patterns
It seems to me that what the “code skeptics” are saying is that if we can account for the origin of the genetic code in terms of either bottom-up processes (e.g. unknown chemical principles that make the code a necessity), or bottom-up constraints (i.e. a kind of selection process that occurred early in the evolution of life, and that favored the code we have now), then we can dispense with the code metaphor. The ultimate explanation for the code has nothing to do with choice or agency; it is ultimately the product of necessity.
In responding to the “code skeptics,” we need to keep in mind that they are bound by their own methodology to explain the origin of the genetic code in non-teleological, causal terms. They need to explain how things happened in the way that they suppose. Thus if a code-skeptic were to argue that living things have the code they do because it is one which accurately and efficiently translates information in a way that withstands the impact of noise, then he/she is illicitly substituting a teleological explanation for an efficient causal one. We need to ask the skeptic: how did Nature arrive at such an ideal code as the one we find in living things today?
By contrast, a “top-down” explanation of life goes beyond such reductionistic accounts. On a top-down account, it makes perfect sense to say that the genetic code has the properties it has because they help it to withstand the impact of noise while accurately and efficiently translating information. The “because” here is a teleological one. A teleological explanation like this ties in perfectly well with intelligent agency: normally the question we ask an agent when they do something is: “Why did you do it that way?” The question of how the agent did it is of secondary importance, and it may be the case that if the agent is a very intelligent one, we might not even understand his/her “How” explanation. But we would still want to know “Why?” And in the case of the genetic code, we have an answer to that question.
We currently lack even a plausible natural process which could have generated the genetic code. On the other hand, we know that intelligent agents can generate codes. The default hypothesis should therefore be that the code we find in living things is the product of an Intelligent Agent.
The question we now have to ask ourselves is whether a teleological account of life implies an Intelligent Designer. Recently, the philosopher Thomas Nagel has argued for a form of teleological naturalism, which I discussed in a recent post. Teleological naturalism at least recognizes the inadequacy of non-purposive causal explanations of the cosmos. That’s a big step in the right direction, and I respect Thomas Nagel for taking that step. Nevertheless, it has a fatal flaw: Nature, being unintelligent, does not and cannot look forward. It is precisely for this reason that the Intelligent Design movement contends that if the genetic code can only be understood from a top-down teleological perspective, then the emergence of the genetic code can only be adequately explained in terms of a Mind which produced it.
Does talk of a “genetic code” beg the question, by assuming the existence of a conscious sender and receiver and a rule-maker?
On Barry Arrington’s post, A dog is a chien is a perro is a hund, Alan Fox objected to talk of a “genetic code” on the grounds that “there is no giver or receiver of information in a communicative sense” (comment 274). He also objected to “rule” terminology on the grounds that it begs the question of the existence of a rule-maker. However, Chance Ratcliff successfully rebutted this objection when he defined the rule using the mathematical notion of a mapping: “the DNA to polypeptide mapping function is in the form F:A→B, where F: is performed essentially by RNA polymerase, aminoacyl trna synthetase, and the ribosome, and works by mechanism to convert elements of A (codons) into elements of B (amino acids)” (comment 308).
Likewise, there is no reason why we cannot speak of a molecule as a sender or receiver of information.
The road ahead
The Wikipedia article on the genetic code mentions five striking facts about the genetic code which any successful account must be able to explain. It seems to me that Intelligent Design would do well to focus on these “nitty-gritty” questions, in order to demonstrate its scientific superiority to “bottom-up,” reductionistic accounts of life. That, for the time being, is the way forward, I believe. If ID proponents can explain a lot more about the peculiar properties of life than their Darwinian counterparts, then the younger generation of scientists, who are not wedded to old dogmas and fossilized ways of thinking, will start to take notice.
What do readers think?
Thanks for the thiughtful post, VJT.
Wonder how you find the time, Vincent? Is all this going into a book à la Mike Gene?
Sorry about the flurry of activity in the thread you discuss, I have been confined to barracks for a couple of days with a bug and time hung heavy.
I’ll just re-make the point that it matters not what you call something (and the genetic code is certainly an amazing something) so long as all agree what is being referred to.
It just seems that some are misled into false conclusions by the mere fact that the storage retrieval aspect of the DNA/RNA/protein pathway is referred to as a”code”. There is the same issue with “junk” DNA. The name was coined and stuck and yet years after, the diverse origins and purposes of non-coding DNA is still a fruitful area of ongoing researh
I found this particularly helpful. It’s a clever slight of hand, is it not? This lead me to another thought. It’s exactly here that the efficacy of natural selection is touted, which is supposed to the the reason we erroneously detect teleology where none exists, and where we’re told to accept material causes for efficient ones. Natural selection, naturally, selects for anything superior with regard to reproductive success, by way of a survival advantage. Because that which survives can reproduce, we can supposedly invite a necessary cause — physical chemistry — to stand in for a sufficient one, or so it’s suggested. (Rather, it’s insisted upon.) But to say that natural selection selects, not only reifies a post hoc observation as a fundamental physical force of the universe, it imputes the primary determination of survival upon something external to the organism, when in actuality it’s the configuration of the organism itself which determines its ability to survive and reproduce. Organisms are contingent, superlatively complex, and it’s their specificity that needs to be accounted for — the ability to survive and reproduce at all, and adapt within their ecological niches, with fabulous plasticity invited by specialized and purposeful adaptional engineering. It won’t do to dismiss life as the necessary result of chemical interactions, just as it wouldn’t fly to reduce computers to the activity of electronic impulses, or grandfather clocks to the operation of Newtonian mechanics.
Thanks VJT, for a fascinating article. I’ll read it again after some beauty sleep.
This logic won’t win any argument, but if evolutionists are actually trying to claim the genetic code is not really a code, but a helpful metaphor to describe it, wow! To me it shows how desperate they are getting.
VJT, if you are not writing a book, do consider so. Sign me up to buy, from now. KF
Alan Fox:
LoL! It’s referred to as a code because it is a code, duh. And you are troubled because your position cannot account for it. Well hey, your position can’t account for anything.
Here I explained why the genetic code is a code, why it implies an overall semiotic system and why both cannot be created by chance and necessity.
I think that when we use the letters A,T,G, and C to represent bases, we are using a code. Futhermore, we could use totally different letters to describe the same piece of DNA.
Supposing we have a machine that reads a text file containing ATGC and produces strands of DNA from them, but that the person who gave us the file has accidentally on purpose swapped each T for a G and vice versa. This wouldn’t be a problem, because we could simply switch them back in a copy of the file or on the fly as we read the original.
Or we could tweak the DNA producing machine so that every time it read a T it actually added a Guanine base instead of a Thymine, and every time it read a G it added a Thymine instead of a Guanine. Then we could maybe implant the resulting DNA into a cell and have it successfully clone itself for generations.
But what if we decided on a third approach – to tweak the cell to work with the switched DNA. Would it then be able make copies of itself – each carrying the new DNA? How much tweaking would be necessary? Would we need to replace loads of things such as (hurredly searches wikipedia) transcription factors which interact with specific stretches of DNA. Would these replacements all play nicely together in the same way without unpleasant side effects? I suspect it would not be possible because I think various new proteins etc. would end up having different physical and chemical properties to the old ones and the physics and the chemistry matter a lot. However, I’m obviously not a biologist, and wouldn’t know where startm but I gather that some of you have the required expertise to pull something like this off 🙂
Alan Fox :
Interactions between molecules involve their chemical properties; charge, conformation, level of hydrophilic and lipophilic residues etc. Nothing analogous to language goes on here. (Comment 118)
DNA sequences translate to specific protein sequences by chemical interactions. (Comment 174)
Apparently what you said could be enough to suggest that there is not a semiotic process going on. If the apparent code is nothing but the result of chemical processes determined by the intrinsic properties of molecules like tRNA and Aminoacyl tRNA synthetase, as you point out, no true interpretation would be carried out.
There is one critical problem on this view. In order for it to be valid, these molecules should have been around before the genetic code existed at all. Nevertheless, these molecules are formed by the same genetic code they are supposed to have created. That is a logical conundrum without solution under a naturalistic approach.
This yEC has a interest because of how DNA is said to be showing a heritage of origins and a control on biology.
I am convinced marsupials are just placentals with pouches.
TRhere is DNA sameness between marsupials and not close between look alike marsupials and placentals.
tHerefore I know DNA is just a points or numbers system.
Its just a code for parts in a universe of a single blueprint.
So likewise man has like DNA with apes just because of like parts. Not being biologically related.
There is no reason to see DNA as evidence of biological relationship.
Just special cases like me and my father because it is so close.
Every other deduction is just a line of reasoning.
DNA is not a code but a parts score.
DNA does not show how biological mechanisms do or could happen.
Its a dull picture of stasis.
So, basically, every line of evidence demonstrates it’s an actual code, and Darwinists, realizing the implications of this, are forced to go into full-blown denier mode. Very telling, indeed.
Alan Fox and company: Would you mind sharing with us why it is you fear the realization that the genetic code is, in fact, an actual code?
Consider someone that finds an unhealthy craving for a bag of Funyuns. And he/she goes to some vending machine and presses the button associated with Funyuns (e.g. B4). The vending mechanism performs several steps to drop the associated/correct bag into the product dispenser. Customer retrieves product.
Is the button matrix an actual semiotic code for individual products/locations? ..or.. Is it only just a matrix sequence where portions of it are merely translated (whatever that means apart from the context of a code) to specific product locations by mechanical interactions.
JGuy
Fox@2:
I’m not sure why you call part of the DNA/RNA/protein pathway as factually a “storage retrieval aspect”. What is being stored and retrieved?
If you say information, then I don’t get how that is consistent with a reductionist position or argument about the genetic code as [factually even] a real code.
JGuy
Alan Fox:
I haven’t been keeping up with all the discussion pertaining to this subject, but at least I know that Alan Fox understands what we mean by ‘arbitrary’.
JGuy at #12
JGuy,
When you drop a coin in the slot of a vending machine, the coin serves as a representation of form (i.e. information). In this instance, the form it represents is a specific monetary value towards the purchase of a product. It serves this role by being identifiable as a particular arrangement of matter. The relationship between the monetary value associated with the representation, and the effect that representation will have on the dispensing of a product, is not established by physical law. Instead it’s established by a second arrangement of matter in the machine. This second arrangement of matter has the capacity to create a specified effect based on the arrangement of the representation. That effect is to establish the otherwise non-existence relationship between the representation and the dispensing of a product. The machine doesn’t know a dime from a dollar, and the entire process follows physical law, but the system incorporates an arbitrary relationship in order to function. The arbitrary relationship is required because ‘collecting the proper monetary value for potato chips’ is not a product of physical law; it’s the product of information. Therefore, the system requires a real capacity to bring that effect into being, based on an arbitrary relationship (as opposed to physical law). It is the absence of an inexorable physical relationship between the representation and its effect that makes the input of form possible. If the arbitrary relationship was not necessary to allow the input of informational constraint on the system, then the price of potato chips could be derived from the material make-up of coins.
JGuy @12:
Interesting example. And I think it highlights how if we are not careful we can trick ourselves into thinking that something so simple just happens naturally. Yet there is that pesky human in your example — the pesky decision maker who seems to be involved at every key step of the process. In your example there is a human that (i) assesses what is needed, (ii) travels to just the right location, (iii) analyzes the possible choices, (iv) makes a selection through some kind of internal decision tree, (v) waits until the selection is properly processed, and (vi) makes use of the retrieved product. (Not to mention all the decisions that went into designing, building and programming the product storage and retrieval machine in the first place.)
There is a very naive view (I’m not saying it is yours, just noting it generally) that stuff in the cell just happens by virtue of raw chemistry. Alan Fox has been making that kind of statement about protein synthesis. That is not only wrong, it is silly if we take a moment to think about it.
Protein synthesis, to pursue the specific example, doesn’t just happen. There are receptors that sense what is needed, switches that control the extent of production, mechanisms that go to the correct location, find the proper string, translate the string, in many cases review and correct the string, in some cases rearrange and concatenate the string to set up a completely different protein, shepherd the completed string to another proper location, assist in folding the string, ascertain whether folding has been properly accomplished, shepherd the completed protein to the right location for end use, help incorporate the protein into a complex of proteins, determine when enough has been produced and provide feedback to the sensors, and so on. The whole process proceeds through a very detailed and sophisticated series of switches, feedback mechanisms and decision trees. And these sensors, switches, feedback mechanisms and decision trees are most certainly operating on the basis of the programming that has been built into them. It is nothing even resembling raw chemistry.
The assertion that what goes on in the cell isn’t based on digital code and decision trees and instruction routines is every bit as silly as someone opening a computer and proclaiming there is no code because, hey, it’s all just electricity flowing around, and after all we all know what electricity does, it just naturally flows through all those wires — given a certain conductor and a certain gradient it just flows; it is purely natural; nothing special about it.
Again, not saying that I think this is your view. Just noting what some folks seem to think.
JG: Let us note, the chaining of bases is through a “standard” link that does not constrain the following base, i.e the base sequence in the chain is highly contingent. It is that sequence that stores information, in a prong-height system similar to Yale lock key prongs. Where also, the way such prongs in a Yale lock work is by interatomic forces tied to complex interactions of electron clouds, i.e generally similar to the types of interactions with R/DNA strands. The tRNA’s have a string that is the anticodon region, which matches the appropriate set of prongs, key-lock style, and then functions as a position-arm device loaded with an Amino Acid that is added to the protein chain under construction in the ribosome. In turn, the tool tip uses a universal CCA coupler and is loaded in the normal case by a specific enzyme that loads the recognised tRNA with the proper protein. Enzymes of course being internal to the protein assembly system, as in chicken and egg here. This system is informational, using recognisable machine code — we have tables that to all intents and purposes look a lot like the ones I used to use with 6800 family microprocessors way back now, the difference being the particular code, not the fact of code. Where also, it has been shown that the tRNA load-out is reprogrammable and the DNA sequence is so programmable that DNA has been used to code information in English. There is no reasonable doubt as to what we are seeing, and so the denial we observe is indeed instructive. There is only one empirically warranted adequate cause of codes, algorithms and associated execution machines, intelligent design by highly skilled and knowledgeable designers. In short, we have every good reason to infer to moral certainty that cell based life, per what we SEE in the living cell, is an artifact. Wisdom, then, is to readjust our views to accord with that reasonable conclusion, or else find compelling empirical evidence that overturns it. The problem on that is that the needle in the haystack results kick in, and the predictable rarity of FSCPO/I in a field of possibilities comes to bear, easily explaining the increasingly severe struggles faced by OOL researchers seeking a blind watchmaker thesis explanation of the credible origin of the living cell. KF
UB:
Right on the money.
EA:
Yes, sometimes it helps to remember that this synthesis process is a part of a much wider co-ordinated system embracing a cellular regulatory circuit/network that is it self a powerful case of nodes and arcs form FSCO/I.
KF
UB@15
The vending machine here requires no coins. The question is more on the relationship of the matrix to the location of the Funyuns. [btw: arguably the most unlikely sentence I ever typed]
JGuy
Eric Anderson @ 16
Thanks for thought out response.
Yeah, I agree. There is a lot more going on than meets the eye. Note my second response to Fox above about the acknowledged fact of a “storage/retrieval” aspect to the DNA/RNA/Protein pathway. The remark about it from Fox seems inconsistent with a simple raw chemical view, as it implies something that isn’t merely raw chemistry.
But I want to comment on the “pesky human”. Most of those steps you mention are irrelevant to the machine itself. The decision making human is simply the analog of some biochemical process that says make more of protein X. But that wasn’t the focus of the thread I thought. The topic was on whether the genetic code was a real semiotic code. So, really we only need to consider from the pushed button to the specific product being activated/dropped.
Consider that that part can all be reduced to entirely raw electro-mechanical interactions (analog to Fox’s plea raw chemical reactions), and do not consider the known origin of the vending machine. We can identify that there is a coding system here (buttons associated with specific products – and even no laws that require the specific associations – i.e. buttons could be hacked & modified to choose any product).
I guess I don’t know where to take that from here anymore. But I thought it made a certain point. That mechanical processes aren’t a whole lot different than chemical processes in how restricted they are to natural laws.
Well, after reading your comment again, I can see that it resonates along the same ideas.
I agree with most here, that the genetic code is a real code. It’s even more glaring when you look, similar to what you said, at the larger more complex context of connected processes.
JGuy
KF@17
Thanks for the response.
Very interesting observation indeed. Jammer made a similar note above.
JGuy
If evolutionists deny that the genetic code is a real code, and choose instead to call it something else like just some chemical reactions. Then this really is instructive, as KF noted above. And as I understand it, it means that it is understood that real code => intelligent design.
But suppose one still denies it is a code on that basis. i.e. That it is all just chemistry. Then what does he/she do with the “codes” that appear to come from the mind of man? Are the codes that man dream up also not codes, but rather just chemical reactions? 😛
JGuy
An artefact brought about by “an agency” I presume.
I wonder what you mean by “an agency”? If you mean God, why not just say so? Even Dawkins allows that he can’t rule that possibility out.
Another alternative is that life was “seeded” here accidentally or deliberately. SETI and Mars exploration may hold future clues to that hypothesis.
It puzzles me that if you have an omnipotent, omniscient “agency” that designed the universe as he wished, why did he not get it right first time. Maybe to acheive its goal, the “agency” cannot tinker. Once the rules are set, it has to work within them. Perhaps it can’t interfere across the reality/imagination border and hence the need for evolution and environmental design.
Interesting. A vending machine without the exchange of money.
No worries, substitute “coin slot” with “keypad” and you end up with the same thing anyway.
🙂
We as agents can order material events – events which operate according to the laws of physics. We can however order the sequence of these events. We can manipulate matter to operate according to our preferred sequences – so it obeys our instructions.
Instructions are specified sequences of events? I’m looking for the right definition…
By ordering events we make computers, vending machines and mobile phones, but how do we order events? Doesn’t this imply a breach of the laws of nature? This question goes back to the phenomenon ‘agency’ – to the mystery that we are.
So code – instructions – refers to agency.
Folks,
After the rhetorical stunt by AF I just had to reply to here, I think that I need to cite the conclusive remarks of that comment, by way of responding here:
So, AF needs to answer to Crick and the others, and to in so doing explain why he is not on the list of Nobel Prize holders.
KF
Alan Fox:
It looks right to me. Could you do better? Very doubtful.
AF,
If you will take a moment to check, you will see that I have specifically not referred to “an agency” but to design.
That is, to a causal process evident form empirically reliable signs, such as FSCO/I as already discussed. Fierst, show that it was arson, then discuss whodunit.
And, you will therefore find nowhere were I have argued that evidence of design for cell based life is direct and decisive evidence of God as designer of the cell. Moreover, you have been around these issues long enough to know that I HAVE SAID JUST THE OPPOSITE, THAT A MOLECULAR NANOTECH LAB SOME GENERATIONS BEYOND VENTER ET AL WOULD BE ADEQUATE CAUSALLY. In which context I have repeatedly pointed out that these investigators have shown that biological design is not only possible but actual.
Where I do say that design inferences point beyond the cosmos to a vastly powerful, knowledgeable and skilled designer is the case of the observed fine tuned cosmos which is set up for C-chemistry, cell based, aqueous medium life, from the first six most abundant elements on down. Which is also the conclusion that many from Hoyle on have drawn and publicly presented, for decades.
And, you will never find me drawing the conclusion on just that that this grounds specific conclusion to the God of various theistic traditions, though I will say that this points in the general direction where such a Being — at least at the level of the God of the philosophers — would be a serious candidate cause.
If you want to know the real — as opposed to strawman — basis on which I know that God is real, in the first instance, absent a miracle of guidance to my mother when I was desperately ill, I would not be here to write this. And, there are many other personal encounters with God in my life, on which basis I have the confidence to take on the crisis that just precipitated itself on my family yesterday.
As to a 101 look at why I am specifically a Christian, in intellectual terms, you may want to look here on and here on in context. But, such is beyond the normal scope of UD as a blog.
I do further believe, and on excellent historical and philosophical grounds, that thinking the Creator’s thoughts after him haws always been and continues to be a valid and sound basis for doing science.
I further hold, on the strength of the logic of necessary and possible being and the evidence that is at stake, that those who deny the actual existence of God (as opposed to emotively, dismiss it) are implying that they hold that God is an impossible being; given the nature of serious candidates to be necessary being, that if possible they are actual. Where also, the formerly favourite problem of evil attempt to show such a God to be impossible, post Platninga’s free will defense, has collapsed. But, as a rule they do not realise this.
So, now, kindly stop the tangential distractions and strawman tactics, and answer to the evidence that points to the genetic code as just that, a code that may be compared directly to letters in text strings.
I have already pointed you to what Sir Francis Crick had to say on March 19, 1953.
Explain to us all, why you seem to disagree with him, on what EMPIRICAL evidence grounds.
KF
Sir Francis Crick, March 19, 1953: “Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)“
Upright BiPed at #15: Well done sir.
Even the form of our coins is arbitrary as is the material from which they are constructed!
When’s the last time you saw a silver quarter or dime or a gold dollar?
But as any good materialist will tell you, it’s just chemistry and no violation of the laws of physics takes place.
I’ve been thinking through the idea of a code and thought I would share a couple of thoughts. I apologize in advance for the length, but wanted to lay this out in some detail. If it too long, the Mods can feel free to post as a head post.
—–
There are a couple of different uses of the word “code.”
1. In one sense, “code” means a written set of instructions to accomplish a task. It is in this sense that a programmer would say he is going to go “write code” or, in current vernacular the word itself has become a verb, so a programmer would generally just say he is going to “code.” Programmers are also sometimes referred to as “coders.”
2. Related to the above meaning, “code” can also mean the particular language or available instruction set that is used in the act of writing code, such as Javascript, C++, Python, Ruby and the like. Each of these is referred to as a “code,” and if I am interested in which instruction set a programmer is using for a particular task it would be perfectly understandable to ask her which code she is using.
3. Code also often has a broader meaning (though it is in fact a closely related meaning — See below*) as a mapping of symbols in one character set to symbols in another character set. For example, Morse Code or the ASCII code.
A subset of this character set mapping is cryptography. This is easy to see in simple cryptography, such as a child’s decoder ring or a simple Caesar cipher (also sometimes referred to as a “Caesar code”). In these simple cases, the same visual characters are used, but they have been reassigned to create a new, arbitrary character set prior to the mapping.
The individual receiving the string can decode the original text if they are given information about how the mapping was performed, or in other words, how the new arbitrary character set was created. This piece of information is called a “key.” For a simple Caesar cipher the key is just an offset number. In more sophisticated forms of cryptography, the new character set can be completely unrelated to the initial set and, one hopes, completely unfathomable to someone looking at the set without the proper key. Indeed, new character sets can be created and mapped to on the fly, so long as the receiver has the proper key to unlock the new character sets.
—–
Now, how does this relate to DNA and what goes on in the cell?
First, the cell clearly operates according to an instruction set. (We are not discussing the origin of that instruction set at this stage, just noting that it exists.) There is mounting evidence that many of the instructions for cellular function reside outside of DNA, but most people would tend to agree that at least a meaningful portion, if not all, of the instruction set of an organism is contained in its DNA. [Note: In a prior thread Nick Matzke, for example, indicated that he thought all the information for an organism was contained in DNA.] Thus, independent of the particular “Genetic Code” discussion, DNA clearly contains a “code” in the sense of an instruction set (#1 above).
Second, there is clearly a mapping of symbols from one character set (nucleotides) to another character set (amino acids). The process is properly referred to as “translation,” because it literally translates a representation in one character set to another character set. The same thing happens when someone receives a series of dots dashes and then translates them into an English sentence based on the Morse Code.
The allegation that this is just chemistry fails, as I have shown in prior comments, both because (i) even the mapping at the most basic level doesn’t just happen by chemistry; there is an arbitrary assignment from one set to another that could have been otherwise and that requires intermediary molecules that have been specifically assigned to perform the translation, and (ii) it is inappropriate to ignore the broader context of the protein synthesis process.
Saying that the translation process in the cell does not use a “code” because it just happens by chemistry is akin to saying that when I open up a file in Word on my computer the ones and zeroes on my hard drive just show up as a coherent English sentence on the screen by dint of physics. After all, one might argue, if there were a different series of ones and zeroes a different sentence might result. This kind of thinking ignores two basic realities: (x) the fact that there is a serious probabilistic hurdle in getting anything intelligible on the screen with a random string of ones and zeroes (the probability/origin-of-string discussion), and (y) the fact that there is a whole system at work to find, retrieve, translate, represent and instantiate the ones and zeroes into something that is meaningful in the new character set (in this case an English sentence).
Getting back to the most basic level of a simple mapping of characters from one set to another set (setting aside for a moment the instruction sets and the broader compute process that the Genetic Code is but a part of), we see that the Genetic Code is properly referred to as a “code.” Every bit as much as the Morse Code or the ASCII code or cryptographic codes.
There is a reason the Genetic Code is called a “code.” And the reason is not for analogy only, nor for convenience of discussion. It is because it is a code.
One may not like the implications, but certainly one of the most interesting questions ever facing humanity has arisen in the last few decades as we have learned about the information and instruction sets and code contained in biology, namely: “What do we make of the fact that there is digitally coded information in life?”
—–
* Programming languages (C++, Ruby, Python, Javascript, etc.) do not constitute a separate realm from the simple mapping concept outlined in #3. In fact, such languages are a subset of the mapping. If we carefully consider what is going on when we write code in a programming language, we see that in fact the entire process is largely one of taking information from one set and translating it into another set.
Allow me to give an example of what I mean:
I have an engineer who needs to monitor the temperature within a server case in order to make sure the system is operating within temperature tolerances. How is this done? Well, in the simplest sense, with a sensor and code.
At its foundation, what is going on is that there is a physical reality (temperature) that is sensed by a physical, analog sensor. That input is then translated into another set (say, an electrical pulse of particular amplitude). That input is then translated into another set, such as a value in a range of possible values. That input will often then be translated into another set, such as an actual temperature profile spectrum. That input will then be translated into binary for storage in the device. That input, when needed, will then be retrieved and translated from binary into Roman numerals using the ASCII character set or code. If desired by the user, those numerals will be translated into either Fahrenheit or Celsius. Without belaboring the details, that input will be translated into a graphic set, then an electrical set, then sent to the monitor for translation into a rendition set, ultimately back to the analog signal that my engineer sees on his screen.
Every programming exercise ultimately boils down to taking an input in one “character set” (whether feedback from the environment, user input, or the computational result of a prior process) and transforming that input within the same character set or translating that input into another set that can be used by the next step of the process. Ultimately, that is what programming is.
U.B. @ 24
Yeah, consider it a perk found in the employee’s break room. 🙂
JGuy
Although I knew that DNA codons are mapped to amino acids, I had no idea that the mapping is completely arbitrary. So that means it’s almost like a 64 box code sheet for sending spy messages, where you can write down whatever word you want in each one. For me, this arbitrariness ends the ‘Is it really a code?’ debate. The mapping is impressive, but this is the clincher. Thank you for this article.
PS: It just struck me that Braille is a useful analogy. Each letter in Braille is made of 3 rows of 2 potential dots. Each of these rows therefore has 4 possible configurations (dot-dot, dot-no dot, no dot-dot, no dot-no dot), analogous to the genetic bases A, C, T, G. But you need a combination of three rows (a codon) to get a letter (an amino acid).
englishmaninistanbul:
Good example with braille. Thanks for bringing that up.
englishmaninistanbul @ 33
I agree that the arbitrary facet helps. It isolates arguments like Fox’s completely. And partly because it allows for the other functional complexity (e.g. error reduction). The code itself is reported in the literature to be better than one in a million randomly generated codes at mitigating copy errors. I think pseudonym Mike Gene suggested possibly even optimum if more factors were considered (but I’m not certain he did).
Anyway, consider if somehow it was not arbitrarily associated. Suppose each nucleotide triplets matched & bound to various point of the specific charges or physical structures of only specific amino acid surface. And somehow all the other functions in the process of translation worked with this (somehow). When considering the big picture of the whole process, how would the mapping still not be classified as a real code? Did Francis Crick understand all the processes of this before he called it a code? I understand this is what A’Fox would probably argue, but it still doesn’t follow when you consider the context of informational transfer.
JGuy
The Braille code comparison seems almost entirely appropriate. Indeed the willful ignorance/blindness on the atheists part reminds me of this passage of scripture:
Notes:
This pointless game, that atheists play, of insanely denying that the genetic code is ‘really’ even a code, has been going on for several years now that I know of. In the following video, Perry Marshall, who works in the communications industry, speaks of going on a atheistic website several years ago and valiantly defending the FACT that the genetic is in fact a code from the insane denialism of many atheists.
I believe this may be the entire video:
Here is Perry’s website:
notes:
It is important to note that, counter-intuitive to materialistic thought (and to every kid who has ever taken a math exam), a computer does not consume energy during computation but will only consume energy when information is erased from it. This counter-intuitive fact is formally known as Landauer’s Principle.
As well, it should be noted that Rolf Landauer himself maintained that the information in a computer was merely ‘physical’. i.e. He held that information in a computer was merely an ’emergent’ property of a material basis, and thus he held that the information programmed into a computer was not really it’s own independent entity. Landauer held this ‘materialistic’ position in spite of objections from people like Roger Penrose who held that information is indeed real and has its own independent existence separate from matter-energy. Landauer held this ‘materialistic’ position since he thought that ‘it ALWAYS took energy to erase information from a computer and therefore the information in the computer must be ‘merely physical’ (merely emergent). Yet the validity of that fairly narrowly focused objection from Landauer, to the reality of ‘transcendent ‘information’ encoded within the computer, has now been overturned, because now information is known to erasable from a computer without consuming energy.
Moreover, to top that off, energy and mass are both now found to reduce to “transcendent” quantum information by quantum teleportation (references upon request). As well, the following paper, alongside the reduction of matter/energy to quantum information in the teleportation experiments, further shows quantum information to be ‘conserved’:
Finding transcendent information to be foundational to reality, in the preceding experiments and proofs, is very suggestive to the Theistic ‘postulation’ of John 1:1 that holds ‘Logos’ (The Word) to be the ultimate foundation of our matter-energy reality in the first place.
Of note, I don’t remember exactly who said this on UD, but I think it is a very profound thought:
Supplemental note:
Music:
p.s. It seems I’m probably underplaying the importance of it being arbitrary. I guess I should emphasis that the arbitrary aspect really could be, as you say, the clincher to it’s codeness.
p.p.s. I guess it seems I really underplayed the importance of arbitrariness. Even though I removed it in my hypothetical, I think I smuggled it back in when I mentioned looking at it in the bigger picture… which, with it’s informational aspects. 😛 Sorry if my posting was at all misleading.
stop misleading us
LOL! I did not mean it that way exactly. How about: “Sorry for selling smuggled goods.” 😀
JGuy
Hello JGuy,
An arbitrary relationship is a fundamental requirement in the operation of any system that produces physical effects from information, as opposed to physical law. It would not be possible to input informational constrtaint into such a system otherwise. Anyone who disputes this has likely not taken the time to study the physical systems involved. They can improve their understanding by considering any concrete physical event not determined by inexorable physical law (such as how many coins to put in a vending machine, or which direction a bee should fly in order to find its food, or when an ant should attack it enemies, or the sequence of amino acids required to transport cargo through a cellular membrane) and then try to devise a system to bring that about by physical law alone. They will find that a context specific (non-physically determined) relationship is a physical requirement.
– – – – – – – – – – – – – –
Hello enblishmanininstanbul,
I too love your example of Braile. Bravo.
The arbitrary nature of the system is a universal observation and a logical necessity. The semiotic manufacture of protein is a physical fact demonstrated by experiment. I agree with you that it is a profound confirmation of a design prediction. I personally belive it’s profound for the very reason that, even among its opponents, it can be articulated without ambiguity – owing to the fact that the biological sciences have confirmed it. Observers can choose to accept the experimental data, or they can side against it. What we are seeing on UD in these past months, are a group of opponents who have (perhaps for the first time) come into direct contact with that decision, and have made their choice.
Their choice doesn’t change the facts. To transfer any form of recorded information (including that within the genome) requires an irreducible core of two material objects in order to input an arbitrary relationship into the output of a system. For those who properly and rationally follow the principle of physical uniformity, that requirement existed at the onset of life as well. Biological organization cannot be demonstrated without it.
Hello Eric,
I like the way you think, and enjoy reading your comments.
UB:
Thank you for your kind words. I think you’ve done an excellent job in numerous posts of articulating some of the most fundamental issues.
—–
Exactly. In fact the ability of a physical medium to hold information is inversely proportional to the law-like structure of that medium.
UB @ 41
Thanks for the thought out response.
I think I got it. As mentioned, I think I smuggled in the arbitrary aspect in my hypothetical when emphasizing the greater context. That is, the arbitrary stuff would then have been smuggled into the overall process as the DNA coded information, even if the genetic code would have been hypothetically determined by physical laws, there would have been an arbitrary element mixed in there. In that scenario, the DNA code would simply follow whatever different pattern determined by the “deterministic code” to make the same protein from the actual/real model.
See if you can help me make sense of this a bit more though.
The real world model is this:
DNA code -> mRNA -> Ribosome (arbitrary Genetic Code) -> Protein.
Hypothetical model:
DNA code -> mRNA -> Ribosome (chemically determined Genetic Code(?)) -> Protein.
In the hypothetical, to achieve the same target protein, the DNA code would simply have to be different to match the non-arbitrary code.
So, my question was, is the Genetic Code not a code in the hypothetical model? My answer to myself was, yeah, it would still be. But I’m open to correction on that.
But even if it would not be, at least there would be a real code in the hypothetical in the form of the DNA code. That is, it would be comprised of arbitrary sequences of information, that “mean” certain proteins.
So, the hypothetical has either one or two real codes, but not zero.
The real world model has at least two codes. The DNA Code (for proteins), and the Genetic Code (for amino acids).
JGuy
p.s. Suppose that we found some physical or chemical pathway whereby you could apply several different influence, each of the same kind, to the initial steps of the pathway and get different results in the product.
So, suppose there were 20 different initial influences we found that would give 20 different results form that process. Then suppose we engineered around this fortuitous process a useful system of encoding. Would then that original deterministic process be imputed with the essense of being a real code because of the mere fact that it was used as one?
Guess in a way I’m just asking the same thing all over again :-/
JGuy
@Upright BiPed
Are you stating that information breaches the principle of physical causal closure? So, besides obeying to physical law, matter obeys to information?
Are you stating that a context specific relationship is by definition non-physical? Are you confining physical law to the inner parts of the ant? So if context is involved in order to explain its behavior it follows a ‘non-physical’ explanation?
Box: engineering is defined as using the materials and forces of nature, intelligently, to design and create things for the benefit of man. Just so, when I type this message, the materials and forces of nature constrain but do not determine the sequence of keys pressed. I choose, and in choosing, I also choose to follow rules and symbols connected to the English language, y no Espanol. The tendency to reduce cause-effect dynamics to material, efficient causes leads to self-referential absurdities by undermining mind and its ability to choose to act rationally. Indeed, the first fact we each experience, is of being a conscious, purposeful, choosing, self-moved person. All other facts we become aware of and reflect upon are brought to us through that first fact. Those who undermine it, therefore refute themselves by reduction to self referential absurdity. In this broad context, we notice that the meaning of the glyphs strung together in this post is assigned by convention, by a code known as written English. That code is not written in the laws and forces of nature, it is a matter of a cumulative choice of English speaking peoples over centuries. Whether we say red or rojo or whatever is not materially determined. KF
JG: The key problem for suggested deterministic models, is that the AA is attached to the tRNA that couples to the codon, through a universal CCA coupler, based on the action of a particular enzyme that serves as loader [notice the chicken-egg cycle involved!]. Indeed, tRNA’s are capable of being re-programmed, as has been done in the lab. The link is INFORMATIONAL, not merely mechanical necessity. KF
@Kairosfocus (46)
Indeed. ‘Sequencing’ and ‘forming’ are good descriptive terms I my opinion. We as agents, as wholes, are living contexts navigating a sea of meaning.
I fully agree. Agency breaches clearly and undeniably the principle of physical causal closure.
So the code is not materially determined because it is the cumulative choice of English speaking agencies. This I find a clear and persuasive argument. I’m not sure however if this corresponds exactly with what UB is saying.
Box: While I wait, UB is speaking about how such codes in the material world are instantiated, transmitted etc using material (and by expression, energy) expressions based on conventional — thus arbitrary — forms. There is no reason why something like a shepherd’s crook standing up with a short cross bar should represent a sound made by putting lower lip under teeth and blowing with the mouth slightly open “ffff . . . ” and there is no reason that his should be a part of a sound pattern that means say a certain annoying insect, a fly; for which other forms are used in other languages. And for that matter, fly means different things in different contexts, e.g. in a certain kind of angling, it means a combination of feathers, hairs, thread etc on a hook that represents a small fish sufficiently to attract a fish to the hook; i.e. a streamer fly. (And that too speaks of how the fish is sensing and responding to patterns that it interprets or its programming interprets as food on the fin trying to get away.) Ink scratches on paper that represent the sounds and words of English are a classic case, ASCII code that does the same is another, and DNA’s genetic code is yet another. KF
kairosfocus, A favor please? This guy has been putting out a series of, what I consider, excellent videos that have been well researched:
micro-RNA and Non-Falsifiable Phylogenetic Trees – video
http://www.youtube.com/watch?v.....hn7gugSY8x
kf, I was wondering if you would be interested in featuring one, or perhaps a few, of this man’s videos on its own blog entry on UD?,, I think the careful work he has done making these informative, fun to watch, videos merits any increased recognition UD may be able to give him.
@Kairosfocus (49)
The text I have written, which you are reading right now, is on its own pure matter. Its origin cannot be explained without agency but now it is pure matter nevertheless.
The question is: how can it contain meaning? The only reason it has meaning right now is because you are reading it. Because your mind is adding meaning to this text. So, besides its origin, meaning needs a mind for its (continued) existence.
– BTW this reminds me of quantum mechanic states which need a mind to become actualized.
The same premise (needing a mind) does not go for e.g. computer code in my opinion. The difference is that we can walk away – thanks to the computer it functions independent from our minds.
Box: The meaning of machine code is built in by its designers, who in effect implement a case structure. On case code X, do action A, in a fetch, decode execute loop. This is given effect through co-ordinated executing machines. The machines that store, transfer, detect case and carry out pre-programmed operations are simply carrying out pre-programmed steps blindly, the smarts lie elsewhere, in the co-ordination that makes these steps in that order on a given machine having particular architecture do something useful. That is, algorithms, data structures, execution units etc all point beyond themselves to a source of the purposeful sequence of actions that are carried out. That is why this is so sensitive an issue for design objectors, as it is very hard indeed to dismiss that sort of context once we see such in action. And, observe how they are utterly at a loss to come up with cases where blind chance and mechanical necessity are observed to achieve this sort of thing. No great surprise, really; given what has been worked out for the 500 bit FSCO/I threshold. KF
BA: interesting. Will follow up further. KF
@Kairosfocus (52)
I know what you are getting at. The thing is however, and I’m sure you agree, that there is a huge difference between machine and agency. This difference is being ignored when you equate case-structures, algorithms, computer code and such with life – like you did in post 52. I understand why you do it; you want to make an argument for intelligent design. For debate strategic purposes you descent to the same level of Darwinists – and agree on a purely mechanistic view on life – in order to drive your point home: it is intelligently designed.
My point is: let’s not forget that life isn’t a machine.
Stephen L. Talbott: “When a single protein can combine with several hundred different modifier molecules, leading to practically infinite combinatorial possibilities, and when that protein itself is an infinitesimal point in the vast, turbulent molecular sea of continual exchange that is the cell, and when the cell is one instance of maybe 100 trillion cells of some 250 different major types in the human body, from muscle to bone, from liver to brain, from blood to retina — well, it’s understandable that many researchers prefer not to stare too long at the larger picture. Nevertheless, we should keep in mind that the collaborative process mentioned above involves not just one table with “negotiators” gathered around it, but countless tables with countless participants and with messages flying back and forth in countless patterns as countless “decisions” are made in a manner somehow subordinated to the unity and multidimensioned interests of the organism as a whole. “
JGuy @43 and 44:
You bring up an excellent issue. Maybe I can rephrase it this way:
If we have an instruction set that selects physical items, where the physical items either pre-exist or automatically come about through purely natural and material processes, does that instruction set constitute a code?
A couple of thoughts:
First, the instruction set would be written in some kind of language. A language is not a physical reality, but is always representative of some reality. So if we have a comprehensible string of representations that either mean something or do something, then in that sense we have a code. Now, we may not think of every language as a code, but in a very real sense that is what a language is: a set of representations that the users, by convention, agree represent certain things.
Second, I’m trying to imagine in my mind’s eye how an instruction set could possibly “select” physical items without some kind of translation process or other implementing program. Let’s take the simplest possible example (which is akin to your hypothetical protein process): say, an instruction set that selects specifically colored blocks from a pile of blocks and puts them in order. Is the instruction set a code? Well, perhaps, in the sense that I’ve outlined above. But there is an additional way in which we may be dealing with code(s).
How are the blocks selected? Well, there has to be some kind of mechnical structure, a machine with an arm, for example, that selects the blocks. And the process of taking an instruction from the instruction set, recognizing the instruction, translating that non-material instruction into a material process involving matter and energy (in this case seeking out, recognizing, moving the arm to grab the block, and moving the block to the appropriate location in the sequence of blocks) is, by definition, a translation of the instruction from the storage medium in which it was writtgn into a physical reality outside of the storage medium.
Thus we see that it is impossible to have a DNA sequence that self-executes. There must be an interpretive/translative process. And this is completely ignoring for a moment the fact that there is a whole parallel process going on to link the amino acids to their receptors. And of course this also ignores the larger context which includes transport, review, repair, folding, and other processes.
None of this just happens by chemistry.
In summary, we have multiple levels of “code” or “language” active in the process of protein synthesis. In several of the instances we clearly have a mapping from one arbitrary character set onto another arbitrary character set (nucleotides to amino acids, for example), which underscores the semiotic aspect of the system in the cell. I’ll leave it to UB to discuss whether he thinks an instruction set selecting from pre-existing items is also an instance of semiosis.
Box @54:
If you mean that life is not only a machine, then fair enough.
But it is certainly instructive to consider life’s machines. Living systems are clearly made up of machines that can be constructed, reverse-engineered, studied and appreciated. We cannot fully understand (or appreciate) life without understanding the machines that make up living systems.
Box:
Pardon, but no.
I am speaking of machines within the cell, and their use of machine code because that is what I am seeing, things that are astonishingly familiar to — but at once far more advanced [self replicating, self maintaining automata using molecular naotech!] than and using significantly different architectures — technologies I work with.
It is not that I want to go to a design inference so I look with the proverbial eye of faith, but that I see the machines and co-ordinated information controlled behaviour that I am so familiar with and am astonished. Maybe, it will help to hear my favourite definition of computer architecture: the assembly language [–> Machine code rendered human-readable] view of the computer.
As to the case structure I pointed out, I am simply saying that the first structure in programming is the sequence of instructions s1s2s3 . . .
In that context, we have an implicit table of instructions [way back, I used just such a table to hand code in machine language for 8-bit microcontroller systems] that the machine is looking for, and in case of sx from the set of possible instructions, it takes up a fetch, decode, execute cycle then proceeds to the next.
The way proteins are assembled is that by the time we have mRNA in a ribosome to synthesise a protein, we have just such a sequence structure in a control tape:
START – s2-s3 . . . sn — STOP
For each sx, there is a corresponding tRNA loaded with a specified AA, and which is then clicked onto the chain of AA’s. There is a ratcheting forward, and the process continues. Until STOP.
This is an algorithmic, step by step finite process that achieves a task.
As has been pointed out the tRNA’s are loaded separately with AA’s by appropriate enzymes, and they carry the AA’s on a universal CCA tool tip. This tip is at the opposite end of the folded tRNA from the anticodon. (It has been demonstrated that tRNA’s can be reloaded with different AA’s, they are inherently reprogrammable, i.e this is not a mechanically forced outcome.)
In the ribosome, the anticodon fits, key-lock style to the mRNA’s active codon, and then the tRNA serves as a position-arm device with a loaded tool-tip. It then clicks the AA to the waiting AA-chain and exits the ribosome.
These are machines, carrying out machine level things using molecular nanotech. This is not the level where agency as such arises. The smarts involved lie in the organisation and the information-rich co-ordination.
Life is not simply a machine, but life uses molecular nanotech machines at cellular level. The chemistry is familiar,t he physics is familiar, and these can be carried out in a test tube or the equivalent.
For that matter, DNA has been coded with information in English.
Why not read and watch here on?
KF
@Eric Anderson (56) Point taken. However the impression still remains that the ID movement puts too much emphasis on the mechanical aspect of life. Typing these words has a distinct machine-like aspect, but that is not the core of what is happening. The true miracle of life is agency and not the mechanical aspect.
@Kairosfocus (57)
Agency – the whole- plays a minor role in your writings. Although you do quote Michael Denton – who clearly expresses awareness of the big mystery of life’s wholeness – saying: “We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison.“ And: “Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell’s manufacturing capability is entirely self-regulated . . . . “
But when we get to Stephen Meyer the focus on agency is totally gone. Life is reduced to matter, energy and information – information rich macromolecules . You summarize Meyer’s ideas like this: “The universe is comprised of matter, energy, and the information that gives order [[better: functional organisation] to matter and energy, thereby bringing life into being. In the cell, information is carried by DNA, which functions like a software program. The signature in the cell is that of the master programmer of life.”
Is there no room for consciousness in the universe?
Where is the acknowledgement of the active whole in your text? Everything that happens in the cell, including the actions of the ribosome, is subordinate to the whole – agency. That is the ultimate mystery of life. There is no level where the whole –agency- is not involved, because there is no level where things can operate uncoordinated. Michael Behe: “The essence of life is regulation: The cell controls how much and what kinds of chemicals it makes; when it loses control, it dies.”
Box:
The whole ID enterprise is about the fact that an agency is required. You know, the “intelligent” part of the “intelligent design” term.
The mechanical part — the machinery — is interesting both because it is a work of engineering art, and because it points to the need for an intelligent agent.
Your quote from Meyer is instructive as an example. You highlighted part of the quote, but forgot to bold the last clause — the one about the master programmer. It seems you have read all the individual words but not understood the broader substance of his argument.
You may rest quite assured that there is no risk the major ID proponents are only focused on the physical and the material. Every discussion, even those discussions focusing heavily on the mechanical structures, is underscored by the larger concept that these things don’t just come about by purely physical and material processes — they require an intelligent agency.
#60
Indeed.
Box,
I have to disagree. It’s exactly the mechanical aspects which allow us to infer design from its physical effects. Without the explicit engineering of these nanotechnological wonders, we wouldn’t be able to call out specified and irreducible complexity. Viewing the cell as a marvel of technological engineering follows from the biological design inference, which is the application of ID methods.
Here is Drew Berry with another slew of what I believe to be the world’s premier biological animations. The material is mind blowing, particularly at 5:00 and on (for the newer material).
BTW “The Machine Metaphor” is certainly not applicable to life as a whole, but it’s hard to deny that the constituents of life’s physical elements are rooted in computational and mechanical realities. The concept of simple, cellular protoplasm has been replaced with the coordinated interplay of countless, purposefully designed parts – motors, signalling systems, transport systems, etc.
ATP Synthase‘s mechanical nature is undeniable, as well as its brilliance, and it is the workhorse producer of the cell’s energy currency.
The visualizations around 7:50 from the above linked Drew Berry video are stunning.
Box: I think we are simply looking at different things and problems. In that light, I am interested in the question of credibly knowing on observable evidence THAT design was or was not credible as causal process. Whodunit is a different issue and not accessible from what we have in hand to address on the material issue. KF
@Eric Anderson (60)
I’m aware that ID requires one intelligent agent – the master designer. But this master programmer is external to the life he creates.
I’m arguing that each organism is an agent on its own – and not just ordered matter and energy, as Stephen Meyer seems to think.
Semi-OT: This video on the bacterial flagellum will have elements that are familiar to many, but gets into some details about the construction process, which is no less remarkable than the structures themselves. Biological videophiles should find this entertaining.
I didn’t realise that ID requires a HE who designed. What if it is Them or even Us or something that we can’t even imagine? As for the DNA being a code, it certainly appears to be so and carry the function of. However, it may also not work in a same way as codes we use, so to say a linear set of instructions. It may be more like a music notation ‘code’. Take a symphony. Play each instrument individually in linear manner. Are you following a ‘code’, well yes, a set of instructions recorded in a form of stave notation, a melody is produced as a result. But its nonsense, the information is only truly understood if it is read at the same time. In mathematics this is also can be demonstrated, its the same in physics etc. Simultaneous function of the entire existence is a vary delicate thing. Maybe we ought to remember that?
I should apologise in advance for my poor English and a great number of errors, English is not my native language.
Hello aham,
The central point of the argument, particularly the semiotic argument, is that the genetic code operates in exactly the same manner as any other form of recorded information. The material conditions are identical.
Box @65:
I agree with you that the question of individual agency is a most interesting question. We could debate for hours, no doubt, about whether “each organism” has agency — each animal, plant, amoeba, etc. But let’s focus on humans for a moment as an example.
Does human agency arise from the human’s composition, from the cells and machines that make up the human? In other words, is our agency (and consciousness, which is closely related) an emergent property of our material makeup?
I don’t think ID is directly relevant to this question, as interesting as the question is. Most Christians, as well as many other faiths, would argue that there is something more to us than just our material makeup — say, a spirit, or a soul, or an intelligence, or something that goes beyond the physical and the material. But again, they would say so on the basis of their religious/philosophical position, not on the basis of ID.
No prominent ID opponent I am aware of takes the position that we are only matter and energy. And your quotes from Meyer certainly don’t state that, so you are misrepresenting his position. Further, prominent ID proponents all agree that humans do have individual agency. Indeed, our experience with human agency is the primary avenue through which we can understand, and analogize, and interpret the fact that there is a broader agency at work in the creation of biological systems.
I don’t mean to be rude and I hope you will take this in a lighthearted spirit, but I have to say it seems that you are itching to pick a fight but don’t have an opponent. So you are grasping at a sentence here or a quote there to try and turn some of the prominent ID proponents (like Meyer, in this instance) into opponents on this issue.
But ID does not speak to the question of whether every organism has agency. Furthermore, every prominent ID proponent agrees that humans have individual agency.
So you are waging a battle over a non-existent dispute.
Tilting at windmills as it were . . .
There’s more to matter than just matter. 🙂